Most Probably Godot is saving or processing your scene in the background. If the scene is too heavy (MB) it takes time to save it. Ideally I always try to keep the debugger open. If this happens too often, try opening the project and the same scene with an external debugger (e.x: VSCode ) with --verbose --stdout --debug flags enabled to see what is going on.
Example: create a launch.json in .vscode folder
{
"name": "Debug Godot Project",
"type": "cppvsdbg",
"request": "launch",
"program": "${workspaceFolder}/bin/godot.exe",
"args": [
"--editor",
"--path",
"[the path to your project root folder]",
"--verbose",
"--debug",
"--stdout"
],
"stopAtEntry": false,
"cwd": "${workspaceFolder}",
"environment": [],
"console": "internalConsole",
"visualizerFile": "${workspaceFolder}/platform/windows/godot.natvis"
//"preLaunchTask": "build godot editor in debug mode"
},